MERFISH Report
1. Overview
1.1 Sample Information
A brief sample information is generated from the submission table for the following analysis.
| Batch | Index | Model | Treatment | region | Data Path |
|---|---|---|---|---|---|
| 1 | C6_PLX_01 | C6 | PLX | region_0 | 202403051612_20240305CarlosPLXm500VZG191x001_VMSC00101 |
| 1 | APP_PLX_01 | APP | PLX | region_1 | 202403051612_20240305CarlosPLXm500VZG191x001_VMSC00101 |
| 1 | APP_Ct_01 | APP | control | region_2 | 202403051612_20240305CarlosPLXm500VZG191x001_VMSC00101 |
| 1 | C6_Ct_01 | C6 | control | region_3 | 202403051612_20240305CarlosPLXm500VZG191x001_VMSC00101 |
| 2 | C6_PLX_02 | C6 | PLX | region_0 | 202403051613_20240305CarlosPLXm500VZG191x002_VMSC05201 |
| 2 | C6_Ct_02 | C6 | control | region_1 | 202403051613_20240305CarlosPLXm500VZG191x002_VMSC05201 |
| 2 | APP_Ct_02 | APP | control | region_2 | 202403051613_20240305CarlosPLXm500VZG191x002_VMSC05201 |
| 2 | APP_PLX_02 | APP | PLX | region_3 | 202403051613_20240305CarlosPLXm500VZG191x002_VMSC05201 |
1.2 MERSCOPE Data Quality Summary
The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.
Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
2. Data Processing
2.1 Cell Segmentation & Quality Control
Based on the spatial information and images obtained from MERFISH, we developed a machine learning model using the Cellpose algorithm to distinguish individual cells via MERFISH DAPI images.
To ensure the data quality and accuracy of cells, we have defined the minimum and maximum values for cell volume and gene count per cell. The cell volume should be between [100, 1800], and the gene count per cell > 25. After filter the outliers, the qualified cells count is shown in the following table.
Outliers were filtered from the data, and the qualified cells count is presented in the following table. The identified cells after filtering are listed in the following table. In total, the study identified 146720 cells across 8 samples. Each sample cell count is shown in table following.
| Sample Index | Cell Count |
|---|---|
| C6_PLX_02 | 31075 |
| C6_Ct_02 | 26774 |
| APP_Ct_02 | 24938 |
| APP_PLX_02 | 18323 |
| C6_Ct_01 | 14779 |
| APP_PLX_01 | 11965 |
| C6_PLX_01 | 10576 |
| APP_Ct_01 | 8290 |
Transcript Count level Violin
Identified Cell Spatial Overview on all Samples
2.2 Dimension Reduction
We use Scanpy for the analysis of single-cell level transcriptome data. The initial stage of our analysis involves the elimination of batch effects, thereby ensuring that different samples from various batches are distributed within the same domain and are statistically reasonable to be integrated and compared. To achieve this, we utilize the Harmony algorithm.
Subsequently, we present visualizations of the batch difference by Leiden UMAP clusters. Also, we illustrate the distributions of the Leiden clusters for future analysis.
Umap of cells and colored by batch
Umap of cells on each batch
Leiden Umap clusters
3. Cell Annotation
We use a recent published tool: Map My Cell to perform cell type annotations for each cell. It is a high resolution cell type annotator build by Alan Institude, with nested levels of classification including 34 classes and 338 subclasses.
The taxonomy is based on the Allen Mouse Brain Common Coordinate Framework version 3 (CCFv3). Part of the used abbreviations is list in the supplementary Abbreviation. Otherwise can be found in CCFv3 paper.
With the annotation, we can identify and plot the selected types of cells in each sample.
Leiden Umap can be dividied to 28 clusters
3.1 Cell Annotation (Low resolution class)
| class_name | count | |
|---|---|---|
| 14 | 31 OPC-Oligo | 31113 |
| 1 | 01 IT-ET Glut | 29120 |
| 15 | 30 Astro-Epen | 22524 |
| 10 | 33 Vascular | 9681 |
| 27 | 18 TH Glut | 7692 |
| 2 | 02 NP-CT-L6b Glut | 7239 |
| 0 | 09 CNU-LGE GABA | 6424 |
| 9 | 34 Immune | 4272 |
| 16 | 12 HY GABA | 3442 |
| 6 | 20 MB GABA | 2853 |
| 5 | 11 CNU-HYa GABA | 2291 |
| 4 | 07 CTX-MGE GABA | 2216 |
| 8 | 27 MY GABA | 2081 |
| 3 | 10 LSX GABA | 1784 |
| 7 | 06 CTX-CGE GABA | 1720 |
| 30 | 14 HY Glut | 1539 |
| 12 | 19 MB Glut | 1351 |
| 19 | 13 CNU-HYa Glut | 1204 |
| 28 | 23 P Glut | 1068 |
| 33 | 17 MH-LH Glut | 1018 |
| 11 | 26 P GABA | 1010 |
| 18 | 32 OEC | 928 |
| 20 | 24 MY Glut | 796 |
| 13 | 05 OB-IMN GABA | 795 |
| 21 | 08 CNU-MGE GABA | 604 |
| 23 | 04 DG-IMN Glut | 499 |
| 31 | 16 HY MM Glut | 466 |
| 17 | 29 CB Glut | 379 |
| 25 | 28 CB GABA | 158 |
| 29 | 21 MB Dopa | 139 |
| 24 | 22 MB-HB Sero | 138 |
| 26 | 03 OB-CR Glut | 104 |
| 22 | 25 Pineal Glut | 56 |
| 32 | 15 HY Gnrh1 Glut | 16 |
3.2 Cell Annotation (High resolution subclass)
| subclass_name | count | |
|---|---|---|
| 43 | 327 Oligo NN | 29245 |
| 52 | 319 Astro-TE NN | 8078 |
| 154 | 151 TH Prkcd Grin2c Glut | 5919 |
| 124 | 333 Endo NN | 5644 |
| 102 | 318 Astro-NT NN | 5425 |
| 44 | 321 Astroependymal NN | 5252 |
| 6 | 006 L4/5 IT CTX Glut | 5233 |
| 16 | 009 L2/3 IT PIR-ENTl Glut | 4415 |
| 2 | 030 L6 CT CTX Glut | 4119 |
| 80 | 062 STR D2 Gaba | 2982 |
| 5 | 004 L6 IT CTX Glut | 2895 |
| 27 | 016 CA1-ProS Glut | 2548 |
| 89 | 334 Microglia NN | 2357 |
| 55 | 017 CA3 Glut | 2268 |
| 76 | 331 Peri NN | 1912 |
| 93 | 061 STR D1 Gaba | 1894 |
| 142 | 326 OPC NN | 1868 |
| 35 | 005 L5 IT CTX Glut | 1621 |
| 10 | 007 L2/3 IT CTX Glut | 1607 |
| 115 | 323 Ependymal NN | 1522 |
| 135 | 325 CHOR NN | 1444 |
| 17 | 014 LA-BLA-BMA-PA Glut | 1347 |
| 28 | 338 Lymphoid NN | 1307 |
| 1 | 022 L5 ET CTX Glut | 1219 |
| 4 | 001 CLA-EPd-CTX Car3 Glut | 1111 |
| 31 | 330 VLMC NN | 1095 |
| 8 | 052 Pvalb Gaba | 1087 |
| 168 | 154 PF Fzd5 Glut | 1075 |
| 19 | 029 L6b CTX Glut | 1057 |
| 69 | 012 MEA Slc17a7 Glut | 1006 |
| 54 | 328 OEC NN | 928 |
| 49 | 093 RT-ZI Gnb3 Gaba | 899 |
| 71 | 101 ZI Pax6 Gaba | 836 |
| 32 | 053 Sst Gaba | 833 |
| 37 | 332 SMC NN | 825 |
| 14 | 046 Vip Gaba | 761 |
| 66 | 064 STR-PAL Chst9 Gaba | 730 |
| 240 | 145 MH Tac2 Glut | 699 |
| 7 | 069 LSX Nkx2-1 Gaba | 697 |
| 100 | 063 STR D1 Sema5a Gaba | 636 |
| 3 | 027 L6b EPd Glut | 630 |
| 36 | 032 L5 NP CTX Glut | 604 |
| 15 | 013 COAp Grxcr2 Glut | 604 |
| 26 | 003 L5/6 IT TPE-ENT Glut | 582 |
| 23 | 337 DC NN | 507 |
| 57 | 010 IT AON-TT-DP Glut | 504 |
| 12 | 002 IT EP-CLA Glut | 498 |
| 98 | 203 LGv-SPFp-SPFm Nkx2-2 Tcf7l2 Gaba | 494 |
| 22 | 049 Lamp5 Gaba | 489 |
| 11 | 028 L6b/CT ENT Glut | 486 |
| 97 | 037 DG Glut | 479 |
| 141 | 025 CA2-FC-IG Glut | 463 |
| 61 | 285 MY Lhx1 Gly-Gaba | 462 |
| 48 | 070 LSX Prdm12 Slit2 Gaba | 454 |
| 204 | 168 SPA-SPFm-SPFp-POL-PIL-PoT Sp9 Glut | 451 |
| 128 | 113 MEA-COA-BMA Ccdc42 Glut | 410 |
| 91 | 306 SPVI-SPVC Sall3 Lhx1 Gly-Gaba | 357 |
| 59 | 114 COAa-PAA-MEA Barhl2 Glut | 355 |
| 29 | 300 PARN-MDRNd-NTS Gbx2 Gly-Gaba | 355 |
| 82 | 041 OB-in Frmd7 Gaba | 329 |
| 209 | 146 LH Pou4f1 Sox1 Glut | 319 |
| 127 | 073 MEA-BST Sox6 Gaba | 315 |
| 63 | 020 L2/3 IT RSP Glut | 306 |
| 21 | 304 NTS-PARN Neurod2 Gly-Gaba | 305 |
| 119 | 079 CEA-BST Six3 Cyp26b1 Gaba | 301 |
| 33 | 202 PRT Tcf7l2 Gaba | 283 |
| 232 | 134 PH-ant-LHA Otp Bsx Glut | 277 |
| 79 | 076 MEA-BST Lhx6 Nfib Gaba | 271 |
| 56 | 047 Sncg Gaba | 269 |
| 200 | 235 PG-TRN-LRN Fat2 Glut | 264 |
| 18 | 071 LSX Prdm12 Zeb2 Gaba | 264 |
| 249 | 129 VMH Nr5a1 Glut | 263 |
| 90 | 320 Astro-OLF NN | 260 |
| 222 | 104 TU-ARH Otp Six6 Gaba | 255 |
| 30 | 201 PAG-RN Nkx2-2 Otx1 Gaba | 254 |
| 189 | 217 PB Lmx1a Glut | 252 |
| 149 | 098 AHN-SBPV-PVHd Pdrm12 Gaba | 250 |
| 123 | 102 DMH-LHA Gsx1 Gaba | 250 |
| 215 | 143 MM-ant Foxb1 Glut | 249 |
| 176 | 317 Astro-CB NN | 247 |
| 88 | 322 Tanycyte NN | 241 |
| 263 | 149 PVT-PT Ntrk1 Glut | 233 |
| 24 | 019 L2/3 IT PPP Glut | 229 |
| 184 | 141 PH-SUM Foxa1 Glut | 227 |
| 96 | 198 IC Six3 En2 Gaba | 217 |
| 190 | 144 MM Foxb1 Glut | 217 |
| 110 | 329 ABC NN | 205 |
| 122 | 210 PRT Mecom Gaba | 204 |
| 205 | 119 SI-MA-LPO-LHA Skor1 Glut | 203 |
| 58 | 068 LSX Otx2 Gaba | 203 |
| 9 | 090 BST-MPN Six3 Nrgn Gaba | 202 |
| 39 | 048 RHP-COA Ndnf Gaba | 201 |
| 53 | 315 DCO UBC Glut | 197 |
| 174 | 152 RE-Xi Nox4 Glut | 196 |
| 77 | 199 PAG-MRN-RN Foxa2 Gaba | 194 |
| 170 | 089 PVR Six3 Sox3 Gaba | 190 |
| 109 | 054 STR Prox1 Lhx6 Gaba | 187 |
| 158 | 107 DMH Hmx2 Gaba | 185 |
| 68 | 039 OB Meis2 Thsd7b Gaba | 185 |
| 147 | 314 CB Granule Glut | 182 |
| 103 | 082 CEA-BST Ebf1 Pdyn Gaba | 177 |
| 25 | 018 L2 IT PPP-APr Glut | 173 |
| 112 | 238 NTS Phox2b Glut | 168 |
| 41 | 033 NP SUB Glut | 162 |
| 106 | 305 SPVI-SPVC Sall3 Nfib Gly-Gaba | 159 |
| 62 | 200 PAG-ND-PCG Onecut1 Gaba | 157 |
| 191 | 222 PB Evx2 Glut | 156 |
| 73 | 051 Pvalb chandelier Gaba | 155 |
| 157 | 074 MEA-BST Lhx6 Sp9 Gaba | 152 |
| 196 | 057 NDB-SI-MA-STRv Lhx8 Gaba | 149 |
| 45 | 278 NLL Gata3 Gly-Gaba | 149 |
| 144 | 080 CEA-AAA-BST Six3 Sp9 Gaba | 146 |
| 78 | 277 DTN-LDT-IPN Otp Pax3 Gaba | 145 |
| 187 | 243 PGRN-PARN-MDRN Hoxb5 Glut | 145 |
| 46 | 050 Lamp5 Lhx6 Gaba | 141 |
| 75 | 023 SUB-ProS Glut | 139 |
| 179 | 215 SNc-VTA-RAmb Foxa1 Dopa | 139 |
| 121 | 216 MB-MY Tph2 Glut-Sero | 138 |
| 64 | 103 PVHd-DMH Lhx6 Gaba | 132 |
| 181 | 108 ARH-PVp Tbx3 Gaba | 126 |
| 120 | 251 NTS Dbh Glut | 125 |
| 99 | 045 OB-STR-CTX Inh IMN | 123 |
| 47 | 195 SNr-VTA Pax5 Npas1 Gaba | 119 |
| 84 | 056 Sst Chodl Gaba | 119 |
| 218 | 221 LDT-PCG Vsx2 Lhx4 Glut | 117 |
| 175 | 181 IC Tfap2d Maf Glut | 116 |
| 172 | 147 AD Serpinb7 Glut | 112 |
| 34 | 265 PB Sst Gly-Gaba | 112 |
| 233 | 088 BST Tac2 Gaba | 111 |
| 87 | 072 LSX Sall3 Lmo1 Gaba | 111 |
| 257 | 150 CM-IAD-CL-PCN Sema5b Glut | 108 |
| 150 | 021 L4 RSP-ACA Glut | 104 |
| 105 | 058 PAL-STR Gaba-Chol | 103 |
| 67 | 034 NP PPP Glut | 103 |
| 164 | 224 PCG-PRNr Vsx2 Nkx6-1 Glut | 102 |
| 95 | 264 PRNc Otp Gly-Gaba | 98 |
| 13 | 194 MRN-VTN-PPN Pax5 Cdh23 Gaba | 98 |
| 116 | 081 ACB-BST-FS D1 Gaba | 96 |
| 111 | 196 PAG-PPN Pax5 Sox21 Gaba | 96 |
| 188 | 205 SC-PAG Lef1 Emx2 Gaba | 92 |
| 20 | 008 L2/3 IT ENT Glut | 91 |
| 152 | 036 HPF CR Glut | 87 |
| 223 | 132 AHN-RCH-LHA Otp Fezf1 Glut | 87 |
| 72 | 011 L2 IT ENT-po Glut | 87 |
| 0 | 065 IA Mgp Gaba | 86 |
| 50 | 283 PRP Otp Gly-Gaba | 86 |
| 108 | 213 SCsg Gabrr2 Gaba | 86 |
| 255 | 173 PAG Pou4f2 Glut | 84 |
| 272 | 167 PRC-PAG Tcf7l2 Irx2 Glut | 81 |
| 40 | 075 MEA-BST Lhx6 Nr2e1 Gaba | 80 |
| 70 | 270 LDT-DTN Gata3 Nfix Gaba | 80 |
| 185 | 263 CS-RPO Meis2 Gaba | 79 |
| 60 | 031 CT SUB Glut | 78 |
| 234 | 206 SCm-PAG Cdh23 Gaba | 75 |
| 195 | 135 STN-PSTN Pitx2 Glut | 75 |
| 220 | 133 PVH-SO-PVa Otp Glut | 74 |
| 156 | 109 LGv-ZI Otx2 Gaba | 74 |
| 166 | 100 AHN Onecut3 Gaba | 73 |
| 148 | 267 CS-PRNr-PCG Tmem163 Otp Gaba | 73 |
| 125 | 085 SI-MPO-LPO Lhx8 Gaba | 73 |
| 118 | 271 NI-RPO Gata3 Nr4a2 Gaba | 70 |
| 65 | 192 PPN-CUN-PCG Otp En1 Gaba | 69 |
| 252 | 123 DMH Nkx2-4 Glut | 69 |
| 138 | 313 CBX Purkinje Gaba | 69 |
| 173 | 208 SC Lef1 Otx2 Gaba | 68 |
| 207 | 139 PH-LHA Foxb1 Glut | 67 |
| 42 | 042 OB-out Frmd7 Gaba | 67 |
| 133 | 106 PVpo-VMPO-MPN Hmx2 Gaba | 66 |
| 155 | 059 GPe-SI Sox6 Cyp26b1 Gaba | 63 |
| 315 | 138 PH Pitx2 Glut | 63 |
| 243 | 127 DMH-LHA Vgll2 Glut | 59 |
| 101 | 043 OB-mi Frmd7 Gaba | 59 |
| 153 | 335 BAM NN | 58 |
| 94 | 262 Pineal Crx Glut | 56 |
| 266 | 105 TMd-DMH Foxd2 Gaba | 56 |
| 194 | 245 SPVI-SPVC Tlx3 Ebf3 Glut | 56 |
| 247 | 125 DMH Hmx2 Glut | 56 |
| 137 | 197 SNr Six3 Gaba | 56 |
| 129 | 067 LSX Sall3 Pax6 Gaba | 55 |
| 146 | 099 SBPV-PVa Six6 Satb2 Gaba | 55 |
| 256 | 097 PVHd-SBPV Six3 Prox1 Gaba | 53 |
| 159 | 182 CUN-PPN Evx2 Meis2 Glut | 51 |
| 291 | 155 PRC-PAG Pax6 Glut | 50 |
| 145 | 268 CS-PRNr-DR En1 Sox2 Gaba | 50 |
| 113 | 246 CU-ECU-SPVI Foxb1 Glut | 49 |
| 126 | 209 SCs Pax7 Nfia Gaba | 49 |
| 92 | 015 ENTmv-PA-COAp Glut | 48 |
| 177 | 299 MARN-PPY Ngfr Gly-Gaba | 48 |
| 38 | 174 PAG Pou4f2 Mesi2 Glut | 48 |
| 211 | 086 MPO-ADP Lhx8 Gaba | 48 |
| 278 | 177 SCig-an-PPT Foxb1 Glut | 48 |
| 313 | 120 MEA Otp Foxp2 Glut | 48 |
| 271 | 124 MPN-MPO-PVpo Hmx2 Glut | 48 |
| 107 | 055 STR Lhx8 Gaba | 46 |
| 219 | 162 CUN Evx2 Lhx2 Glut | 45 |
| 214 | 229 PB-NTS Phox2b Ebf3 Lmx1b Glut | 44 |
| 151 | 293 PAS-MV Ebf2 Gly-Gaba | 44 |
| 239 | 164 APN C1ql4 Glut | 44 |
| 246 | 092 TMv-PMv Tbx3 Hist-Gaba | 43 |
| 136 | 207 SCs Dmbx1 Gaba | 43 |
| 51 | 336 Monocytes NN | 43 |
| 192 | 248 MV-SPIV Zic4 Neurod2 Glut | 43 |
| 169 | 193 MRN-PPN-CUN Pax8 Gaba | 43 |
| 251 | 128 VMH Fezf1 Glut | 43 |
| 182 | 290 MY Prox1 Lmo7 Gly-Gaba | 42 |
| 183 | 286 PPY-PGRNl Vip Glyc-Gaba | 40 |
| 161 | 214 IPN Otp Crisp1 Gaba | 38 |
| 167 | 204 SC Otx2 Gcnt4 Gaba | 37 |
| 180 | 087 MPN-MPO-LPO Lhx6 Zfhx3 Gaba | 37 |
| 83 | 261 HB Calcb Chol | 36 |
| 74 | 254 VCO Mafa Meis2 Glut | 36 |
| 269 | 094 SCH Six6 Cdc14a Gaba | 36 |
| 258 | 308 DCO Il22 Gly-Gaba | 36 |
| 290 | 228 PSV Pvalb Lhx2 Glut | 34 |
| 237 | 130 LHA Pmch Glut | 33 |
| 259 | 172 PAG Pou4f1 Ebf2 Glut | 33 |
| 117 | 060 OT D3 Folh1 Gaba | 33 |
| 213 | 287 MV-SPIV-PRP Dmbx1 Gly-Gaba | 33 |
| 143 | 272 LDT-PCG-CS Gata3 Lhx1 Gaba | 33 |
| 285 | 160 PAG-SC Neurod2 Meis2 Glut | 32 |
| 163 | 303 IRN Dmbx1 Pax2 Gly-Gaba | 32 |
| 284 | 121 MEA-BST Otp Zic2 Glut | 31 |
| 104 | 282 POR Spp1 Gly-Gaba | 30 |
| 282 | 111 TRS-BAC Sln Glut | 30 |
| 283 | 316 Bergmann NN | 30 |
| 279 | 148 AV Col27a1 Glut | 30 |
| 206 | 083 CEA-BST Rai14 Pdyn Crh Gaba | 30 |
| 134 | 191 PAG-MRN Rln3 Gaba | 29 |
| 254 | 212 SCs Lef1 Gli3 Gaba | 29 |
| 298 | 066 NDB-SI-ant Prdm12 Gaba | 28 |
| 216 | 159 IF-RL-CLI-PAG Foxa1 Glut | 28 |
| 131 | 276 LDT-PCG St18 Gaba | 27 |
| 235 | 115 MS-SF Bsx Glut | 27 |
| 276 | 137 PH-an Pitx2 Glut | 25 |
| 193 | 309 CB PLI Gly-Gaba | 25 |
| 288 | 091 ARH-PVi Six6 Dopa-Gaba | 25 |
| 186 | 324 Hypendymal NN | 25 |
| 244 | 170 PAG-MRN Tfap2b Glut | 25 |
| 130 | 044 OB Dopa-Gaba | 24 |
| 268 | 180 SCiw Pitx2 Glut | 23 |
| 132 | 257 SPVC Ccdc172 Glut | 23 |
| 178 | 095 DMH Prdm13 Gaba | 23 |
| 86 | 211 SC Tnnt1 Gli3 Gaba | 23 |
| 197 | 279 PSV Pax2 Gly-Gaba | 23 |
| 286 | 226 PRNc-PARN Tlx1 Glut | 23 |
| 229 | 117 LHA Barhl2 Glut | 22 |
| 228 | 225 PRNc-NI-SG-RPO Vsx2 Nr4a2 Glut | 21 |
| 250 | 126 ARH-PVp Tbx3 Glut | 20 |
| 308 | 026 NLOT Rho Glut | 20 |
| 302 | 038 DG-PIR Ex IMN | 20 |
| 289 | 131 LHA-AHN-PVH Otp Trh Glut | 20 |
| 264 | 284 GRN-IRN-MDRNd Ikzf1 Gly-Gaba | 20 |
| 296 | 156 MB-ant-ve Dmrta2 Glut | 20 |
| 241 | 118 ADP-MPO Trp73 Glut | 19 |
| 217 | 165 PAG-MRN Pou3f1 Glut | 19 |
| 262 | 153 MG-POL-SGN Nts Glut | 19 |
| 231 | 171 PAG Pou4f1 Bnc2 Glut | 19 |
| 270 | 116 AVPV-MEPO-SFO Tbr1 Glut | 18 |
| 293 | 122 LHA-MEA Otp Glut | 18 |
| 292 | 169 PAG-SC Pou4f1 Zic1 Glut | 18 |
| 236 | 140 PMd-LHA Foxb1 Glut | 18 |
| 140 | 291 NTS-MDRNd Prox1 Zic1 Gly-Gaba | 18 |
| 198 | 163 APN C1ql2 Glut | 17 |
| 238 | 296 RPA Pax6 Hoxb5 Gly-Gaba | 17 |
| 160 | 231 IPN-LDT Vsx2 Nkx6-1 Glut | 17 |
| 225 | 035 OB Eomes Ms4a15 Glut | 17 |
| 199 | 247 MV-SPIV Phox2b Ebf3 Lbx1 Glut | 17 |
| 139 | 256 SPVC Mafa Glut | 17 |
| 208 | 142 HY Gnrh1 Glut | 16 |
| 212 | 237 PRP-NI-PRNc-GRN Otp Glut | 16 |
| 267 | 176 SCig Foxb1 Glut | 16 |
| 314 | 077 CEA-BST Gal Avp Gaba | 15 |
| 309 | 112 GPi Tbr1 Cngb3 Gaba-Glut | 15 |
| 224 | 136 PMv-TMv Pitx2 Glut | 15 |
| 227 | 275 PDTg Otp Olig3 Gaba | 14 |
| 210 | 310 CBX Golgi Gly-Gaba | 14 |
| 81 | 302 MV Xdh Gly-Gaba | 14 |
| 295 | 244 MV-SPIV Slc6a2 Glut | 13 |
| 277 | 184 PAG Tcf24 Glut | 13 |
| 171 | 273 PDTg-PCG Pax6 Gaba | 12 |
| 261 | 175 SC Bnc2 Glut | 12 |
| 317 | 190 ND-INC Foxd2 Glut | 10 |
| 85 | 298 PRP Gata3 Slc6a5 Gly-Gaba | 10 |
| 287 | 307 RO-RPA Pkd2l1 Gaba | 10 |
| 242 | 295 CBN Dmbx1 Gaba | 10 |
| 165 | 078 SI-MA-ACB Ebf1 Bnc2 Gaba | 10 |
| 253 | 232 LDT Vsx2 Nkx6-1 Nfib Glut | 9 |
| 275 | 312 CBX MLI Cdh22 Gaba | 9 |
| 319 | 253 IO Fgl2 Glut | 9 |
| 203 | 258 SPVC Nmu Glut | 9 |
| 273 | 220 PB Pax5 Glut | 9 |
| 201 | 255 SPVO Mafa Meis2 Glut | 9 |
| 305 | 084 BST-SI-AAA Six3 Slc22a3 Gaba | 9 |
| 310 | 187 SCsg Pde5a Glut | 9 |
| 265 | 223 B-PB Nr4a2 Glut | 9 |
| 297 | 166 MRN Pou3f1 C1ql4 Glut | 8 |
| 248 | 110 BST-po Iigp1 Glut | 8 |
| 230 | 252 DMX VII Tbx20 Chol | 8 |
| 114 | 297 CU-ECU Pax2 Gly-Gaba | 8 |
| 226 | 281 POR Gata3 Gly-Gaba | 8 |
| 221 | 040 OB Trdn Gaba | 8 |
| 162 | 178 SCig Foxb1 Otx2 Glut | 8 |
| 320 | 250 CBN Neurod2 Pvalb Glut | 7 |
| 294 | 179 SCdg-PAG Tfap2b Glut | 7 |
| 260 | 234 MEV Ppp1r1c Glut | 6 |
| 202 | 289 MDRNd Prox1 Pax6 Gly-Gaba | 5 |
| 306 | 311 CBX MLI Megf11 Gaba | 5 |
| 321 | 161 PAG Pou4f3 Glut | 5 |
| 300 | 233 NLL-SOC Spp1 Glut | 5 |
| 303 | 269 LDT Fgf7 Gaba | 5 |
| 281 | 096 PVHd Gsc Gaba | 5 |
| 245 | 239 MARN-GRN Pyy Glut | 3 |
| 304 | 230 PRNr Otp Nfib Glut | 3 |
| 301 | 249 NTS Aldh1a2 Glut | 3 |
| 312 | 188 SCop Sln Glut | 2 |
| 311 | 274 PDTg Otp Shroom3 Gaba | 2 |
| 299 | 024 L5 PPP Glut | 2 |
| 280 | 236 IRN Vip Glut | 2 |
| 318 | 288 MDRN Hoxb5 Ebf2 Gly-Gaba | 2 |
| 274 | 158 MRN-PAG Nkx6-1 Glut | 2 |
| 307 | 294 MV Pax6 Gly-Gaba | 2 |
| 322 | 218 PSV Lmx1a Trpv6 Glut | 2 |
| 325 | 301 MV Nr4a2 Gly-Gaba | 1 |
| 326 | 186 SCop Pou4f2 Neurod2 Glut | 1 |
| 316 | 292 MV Nkx6-1 Gly-Gaba | 1 |
| 324 | 227 PB-PSV Phox2b Glut | 1 |
| 323 | 240 MDRNv Lhx4 Qrfprl Glut | 1 |
| 327 | 260 MDRNv Crp Glut | 1 |
3.3 Custome-selected cell type
To ensure accuracy, we exclude cells that are identified by map my cell but have less than 1% distribution in Leiden clusters. In this way, Additionally, we select specific target cell types and an appropriate resolution level that is suitable for our research purposes.
| APP_Ct_01 | APP_Ct_02 | APP_PLX_01 | APP_PLX_02 | C6_Ct_01 | C6_Ct_02 | C6_PLX_01 | C6_PLX_02 | |
|---|---|---|---|---|---|---|---|---|
| Astrocyte | 591 | 3131 | 805 | 2501 | 983 | 4358 | 361 | 5726 |
| CA1-ProS Glut | 190 | 577 | 56 | 252 | 336 | 295 | 207 | 575 |
| CA2 Glut | 45 | 89 | 31 | 49 | 61 | 57 | 28 | 89 |
| CA3 Glut | 78 | 347 | 67 | 330 | 246 | 240 | 195 | 701 |
| DG Glut | 12 | 131 | 13 | 84 | 36 | 66 | 27 | 118 |
| Endo | 114 | 1337 | 111 | 939 | 247 | 1059 | 58 | 1710 |
| HY GABA | 139 | 459 | 539 | 448 | 450 | 540 | 314 | 381 |
| HY Glut | 76 | 131 | 135 | 261 | 178 | 328 | 157 | 664 |
| L2 Glut | 27 | 23 | 56 | 17 | 47 | 23 | 30 | 28 |
| L2/3 Glut | 516 | 1257 | 880 | 351 | 922 | 1046 | 535 | 939 |
| L4 Glut | 16 | 8 | 14 | 5 | 4 | 45 | 5 | 1 |
| L4/5 Glut | 590 | 707 | 1042 | 529 | 940 | 445 | 484 | 296 |
| L5 Glut | 423 | 385 | 480 | 240 | 550 | 443 | 474 | 267 |
| L5/6 Glut | 76 | 49 | 66 | 27 | 94 | 81 | 89 | 84 |
| L6 Glut | 316 | 311 | 390 | 259 | 470 | 355 | 366 | 324 |
| L6b Glut | 487 | 869 | 614 | 709 | 729 | 891 | 812 | 886 |
| MB GABA | 168 | 430 | 323 | 312 | 262 | 580 | 254 | 457 |
| MB Glut | 35 | 140 | 63 | 276 | 69 | 348 | 76 | 293 |
| Microglia | 201 | 699 | 19 | 2 | 243 | 1086 | 1 | 15 |
| OPC | 102 | 448 | 22 | 153 | 274 | 526 | 26 | 266 |
| Oligo | 913 | 5146 | 1255 | 4213 | 1688 | 6049 | 1251 | 7360 |
| STR D1 GABA | 172 | 500 | 604 | 351 | 258 | 321 | 191 | 101 |
| STR D2 GABA | 205 | 525 | 516 | 540 | 349 | 460 | 278 | 50 |
| SUB-Pros Glut | 13 | 13 | 16 | 4 | 9 | 63 | 10 | 9 |
| TH Glut | 473 | 1302 | 344 | 1192 | 1160 | 949 | 840 | 1317 |
| VLMC | 48 | 136 | 23 | 130 | 78 | 156 | 25 | 459 |
3.4 Scaled Cell Count heatmap
Cell Proportion Heatmap
4. Spatial Visualization
4.1 Neurons
4.2 Non-Neurons
4.3 Microglia Gene Markers
5. Hippocampal Region Selection
5.1 Hippocampal Region Cell Count
| Counts | |
|---|---|
| APP_Ct_01 | 3880 |
| APP_Ct_02 | 3241 |
| APP_PLX_01 | 2305 |
| APP_PLX_02 | 1959 |
| C6_Ct_01 | 5786 |
| C6_Ct_02 | 3350 |
| C6_PLX_01 | 3363 |
| C6_PLX_02 | 4418 |
5.2 Hippocampal Spatial Visualization
6. Gene differentiation
6.1 Hippocampal
Here, we use Wilcoxon rank-sum to compute differential expression.
The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.
6.1.1 APP only, PLX v.s. control
Cell number compare: ‘PLX’: 4264 ; ‘Control’: 7121
## [1] 4264
## [1] 7121
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 470 | Csf1r | -9.992595 | -8.497447 | 0.0000000 | 0.0000000 |
| 466 | App | -9.321175 | -7.206883 | 0.0000000 | 0.0000000 |
| 459 | Selplg | -8.342670 | -6.263949 | 0.0000000 | 0.0000000 |
| 467 | Ctss | -9.638645 | -5.085486 | 0.0000000 | 0.0000000 |
| 441 | C1qa | -6.676291 | -5.084176 | 0.0000000 | 0.0000000 |
| 434 | Tmem119 | -5.920957 | -4.544962 | 0.0000000 | 0.0000000 |
| 6 | Penk | 7.467743 | 4.347895 | 0.0000000 | 0.0000000 |
| 4 | Adora2a | 8.577372 | 3.707588 | 0.0000000 | 0.0000000 |
| 442 | Inpp5d | -6.713989 | -3.474978 | 0.0000000 | 0.0000000 |
| 488 | Egr1 | -12.467212 | -3.430572 | 0.0000000 | 0.0000000 |
| 427 | Cx3cr1 | -5.433567 | -3.349348 | 0.0000001 | 0.0000003 |
| 498 | Slc17a7 | -18.380058 | -3.326372 | 0.0000000 | 0.0000000 |
| 10 | Ppp1r1b | 5.211143 | 2.990984 | 0.0000002 | 0.0000011 |
| 457 | Grin1 | -8.249740 | -2.755692 | 0.0000000 | 0.0000000 |
| 348 | Itgam | -2.424661 | -2.656466 | 0.0153227 | 0.0445427 |
| 9 | Drd2 | 5.634256 | 2.620728 | 0.0000000 | 0.0000001 |
| 387 | Siglech | -3.582790 | -2.600245 | 0.0003399 | 0.0013075 |
| 482 | Dnm1 | -11.955046 | -2.572117 | 0.0000000 | 0.0000000 |
| 476 | Syp | -10.921723 | -2.533255 | 0.0000000 | 0.0000000 |
| 5 | Six3 | 7.919350 | 2.530318 | 0.0000000 | 0.0000000 |
| 480 | Apoe | -11.712777 | -2.436881 | 0.0000000 | 0.0000000 |
| 1 | Syndig1l | 11.199730 | 2.429623 | 0.0000000 | 0.0000000 |
| 411 | Trem2 | -4.667787 | -2.339870 | 0.0000030 | 0.0000148 |
| 391 | Plp1 | -3.813616 | 2.281649 | 0.0001369 | 0.0005434 |
| 11 | Otof | 4.848666 | 2.204886 | 0.0000012 | 0.0000066 |
| 499 | Camk2a | -19.099926 | -2.200464 | 0.0000000 | 0.0000000 |
| 495 | Arc | -15.471355 | -2.044732 | 0.0000000 | 0.0000000 |
| 485 | Vgf | -12.289746 | -2.035441 | 0.0000000 | 0.0000000 |
| 496 | Dkk3 | -15.656831 | -2.028133 | 0.0000000 | 0.0000000 |
| 492 | Syngap1 | -14.241967 | -1.949083 | 0.0000000 | 0.0000000 |
| 2 | C4b | 10.918763 | 1.898962 | 0.0000000 | 0.0000000 |
| 14 | Scn4b | 4.658997 | 1.884755 | 0.0000032 | 0.0000153 |
| 0 | Gfap | 17.104430 | 1.747727 | 0.0000000 | 0.0000000 |
| 493 | Dlg4 | -14.311377 | -1.746045 | 0.0000000 | 0.0000000 |
| 468 | Ptpru | -9.713569 | -1.710330 | 0.0000000 | 0.0000000 |
| 373 | P2ry12 | -3.117066 | -1.664990 | 0.0018266 | 0.0063424 |
| 483 | Cx3cl1 | -12.080276 | -1.662768 | 0.0000000 | 0.0000000 |
| 431 | Nptx2 | -5.712518 | -1.612757 | 0.0000000 | 0.0000001 |
| 430 | Cckbr | -5.684848 | -1.510544 | 0.0000000 | 0.0000001 |
| 453 | Grin2a | -7.467175 | -1.499516 | 0.0000000 | 0.0000000 |
| 376 | Gria1 | -3.156925 | -1.480083 | 0.0015944 | 0.0056540 |
| 461 | Epha10 | -8.605890 | -1.440944 | 0.0000000 | 0.0000000 |
| 491 | Syn1 | -13.488163 | -1.440494 | 0.0000000 | 0.0000000 |
| 350 | Rspo1 | -2.483363 | -1.434904 | 0.0130148 | 0.0385054 |
| 494 | Bin1 | -14.323399 | -1.424151 | 0.0000000 | 0.0000000 |
| 436 | Gm2115 | -6.024242 | -1.398714 | 0.0000000 | 0.0000000 |
| 455 | Nptx1 | -7.868817 | -1.389696 | 0.0000000 | 0.0000000 |
| 481 | Nr4a1 | -11.898462 | -1.382180 | 0.0000000 | 0.0000000 |
| 465 | Bcan | -9.280068 | -1.340949 | 0.0000000 | 0.0000000 |
| 497 | Sorl1 | -16.587605 | -1.336206 | 0.0000000 | 0.0000000 |
| 489 | Cck | -12.516647 | -1.297370 | 0.0000000 | 0.0000000 |
| 421 | Ptk2b | -5.111560 | -1.292715 | 0.0000003 | 0.0000018 |
| 361 | Abi3 | -2.818073 | -1.290162 | 0.0048313 | 0.0153862 |
| 478 | Rph3a | -11.049101 | -1.284928 | 0.0000000 | 0.0000000 |
| 484 | Mapt | -12.197148 | -1.249153 | 0.0000000 | 0.0000000 |
| 413 | Plcxd2 | -4.711940 | -1.229122 | 0.0000025 | 0.0000123 |
| 490 | Lynx1 | -13.287546 | -1.228083 | 0.0000000 | 0.0000000 |
| 379 | Plcg2 | -3.369969 | -1.222410 | 0.0007518 | 0.0027238 |
| 419 | Adrb1 | -4.862046 | -1.209240 | 0.0000012 | 0.0000063 |
| 13 | Drd1 | 4.707247 | 1.205178 | 0.0000025 | 0.0000124 |
| 8 | Meis2 | 6.155312 | 1.198299 | 0.0000000 | 0.0000000 |
| 447 | Nr4a2 | -7.062252 | -1.190020 | 0.0000000 | 0.0000000 |
| 352 | Ace | -2.492969 | -1.163853 | 0.0126680 | 0.0379395 |
| 450 | Eno2 | -7.358470 | -1.162827 | 0.0000000 | 0.0000000 |
| 486 | Slc30a3 | -12.291239 | -1.149618 | 0.0000000 | 0.0000000 |
| 18 | Clic6 | 2.492862 | -1.145236 | 0.0126718 | 0.0379395 |
| 460 | Brinp1 | -8.353975 | -1.138802 | 0.0000000 | 0.0000000 |
| 456 | Zbtb20 | -8.184727 | -1.123504 | 0.0000000 | 0.0000000 |
| 382 | Olig1 | -3.428355 | -1.115202 | 0.0006073 | 0.0022491 |
| 479 | Nptxr | -11.069632 | -1.105270 | 0.0000000 | 0.0000000 |
| 443 | Fibcd1 | -6.756305 | -1.102211 | 0.0000000 | 0.0000000 |
| 414 | Grin2b | -4.727474 | -1.049061 | 0.0000023 | 0.0000115 |
| 403 | Kcnh7 | -4.342469 | -1.021783 | 0.0000141 | 0.0000629 |
| 358 | Htr1a | -2.690160 | -1.021183 | 0.0071418 | 0.0223181 |
| 364 | Celsr1 | -2.878600 | -1.013014 | 0.0039944 | 0.0129186 |
| 463 | Fam131a | -9.033947 | -1.009017 | 0.0000000 | 0.0000000 |
6.1.2 C6 only, PLX v.s. control
Cell number compare: ‘PLX’: 7781 ; ‘Control’: 9136
## [1] 7781
## [1] 9136
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 2 | App | 12.126558 | 7.122068 | 0.0000000 | 0.0000000 |
| 497 | Csf1r | -11.103088 | -5.479664 | 0.0000000 | 0.0000000 |
| 496 | Selplg | -9.522469 | -5.325641 | 0.0000000 | 0.0000000 |
| 474 | Clic6 | -2.712040 | -4.972346 | 0.0066871 | 0.0288235 |
| 499 | Ctss | -12.829632 | -4.522893 | 0.0000000 | 0.0000000 |
| 494 | C1qa | -7.416728 | -3.832811 | 0.0000000 | 0.0000000 |
| 493 | Tmem119 | -6.366945 | -3.800780 | 0.0000000 | 0.0000000 |
| 470 | Ccdc153 | -2.569087 | -3.144938 | 0.0101967 | 0.0401444 |
| 495 | Inpp5d | -7.445282 | -2.828421 | 0.0000000 | 0.0000000 |
| 492 | Cx3cr1 | -5.666165 | -2.750329 | 0.0000000 | 0.0000001 |
| 1 | Syp | 14.604422 | 2.616693 | 0.0000000 | 0.0000000 |
| 491 | Trem2 | -5.078127 | -2.560248 | 0.0000004 | 0.0000034 |
| 498 | Apoe | -12.014446 | -2.503629 | 0.0000000 | 0.0000000 |
| 480 | Siglech | -3.225496 | -2.325987 | 0.0012575 | 0.0066891 |
| 61 | Bsg | 3.832298 | 1.912956 | 0.0001270 | 0.0008138 |
| 28 | Gfap | 6.662101 | 1.887792 | 0.0000000 | 0.0000000 |
| 0 | Camk2a | 16.020320 | 1.604297 | 0.0000000 | 0.0000000 |
| 7 | Ptk2b | 9.662978 | 1.584093 | 0.0000000 | 0.0000000 |
| 19 | Nptx1 | 8.224086 | 1.530522 | 0.0000000 | 0.0000000 |
| 4 | Slc17a7 | 11.085380 | 1.456908 | 0.0000000 | 0.0000000 |
| 488 | Plcg2 | -4.409460 | -1.430689 | 0.0000104 | 0.0000773 |
| 477 | Pdgfra | -2.751270 | -1.365383 | 0.0059365 | 0.0262676 |
| 472 | Folr1 | -2.639988 | -1.289205 | 0.0082909 | 0.0342599 |
| 6 | Grin1 | 10.691108 | 1.288557 | 0.0000000 | 0.0000000 |
| 487 | Ppp1r1b | -4.263815 | -1.284282 | 0.0000201 | 0.0001456 |
| 87 | Klf4 | 2.776866 | 1.207321 | 0.0054886 | 0.0249481 |
| 82 | Klf2 | 2.889777 | 1.203468 | 0.0038552 | 0.0185344 |
| 10 | Dnm1 | 9.490662 | 1.200793 | 0.0000000 | 0.0000000 |
| 21 | Cpne6 | 7.658239 | 1.175915 | 0.0000000 | 0.0000000 |
| 27 | Nr4a1 | 6.812413 | 1.135059 | 0.0000000 | 0.0000000 |
| 26 | Dkk3 | 6.874430 | 1.044996 | 0.0000000 | 0.0000000 |
| 29 | Zbtb20 | 6.594520 | 1.034572 | 0.0000000 | 0.0000000 |
| 24 | Vgf | 6.904668 | 1.012222 | 0.0000000 | 0.0000000 |
6.1.3 Control only, APP v.s. C6
Cell number compare: ‘APP’: 7121 ; ‘C6’: 9136
## [1] 7121
## [1] 9136
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 495 | Plp1 | -8.300681 | -6.447118 | 0.0000000 | 0.0000000 |
| 70 | App | 6.985622 | 4.658610 | 0.0000000 | 0.0000000 |
| 12 | Egr1 | 18.427420 | 3.835128 | 0.0000000 | 0.0000000 |
| 10 | Grin1 | 18.693602 | 3.700864 | 0.0000000 | 0.0000000 |
| 487 | Prkcd | -6.147834 | -2.912895 | 0.0000000 | 0.0000000 |
| 3 | Slc17a7 | 21.532150 | 2.850603 | 0.0000000 | 0.0000000 |
| 0 | Camk2a | 30.099354 | 2.789707 | 0.0000000 | 0.0000000 |
| 9 | Ptk2b | 18.825884 | 2.732910 | 0.0000000 | 0.0000000 |
| 7 | Nptx1 | 19.462187 | 2.729362 | 0.0000000 | 0.0000000 |
| 2 | Nptxr | 23.599588 | 2.588226 | 0.0000000 | 0.0000000 |
| 14 | Dnm1 | 17.780014 | 2.525539 | 0.0000000 | 0.0000000 |
| 1 | Dlg4 | 24.022236 | 2.403585 | 0.0000000 | 0.0000000 |
| 6 | Grin2a | 19.557583 | 2.368127 | 0.0000000 | 0.0000000 |
| 21 | Syp | 14.829331 | 2.209733 | 0.0000000 | 0.0000000 |
| 44 | Nr4a2 | 9.675894 | 2.202026 | 0.0000000 | 0.0000000 |
| 4 | Syngap1 | 20.664804 | 2.169545 | 0.0000000 | 0.0000000 |
| 488 | Agt | -6.226850 | -2.138840 | 0.0000000 | 0.0000000 |
| 497 | Apoe | -9.418557 | -2.085650 | 0.0000000 | 0.0000000 |
| 5 | Grin2b | 20.256319 | 2.083073 | 0.0000000 | 0.0000000 |
| 499 | Gfap | -16.051336 | -2.063672 | 0.0000000 | 0.0000000 |
| 485 | Synpo2 | -4.845045 | -2.053212 | 0.0000013 | 0.0000054 |
| 27 | Nr4a1 | 13.733349 | 1.992821 | 0.0000000 | 0.0000000 |
| 20 | Arc | 14.955062 | 1.929970 | 0.0000000 | 0.0000000 |
| 494 | Tcf7l2 | -8.215328 | -1.911108 | 0.0000000 | 0.0000000 |
| 59 | Cckbr | 8.238744 | 1.870255 | 0.0000000 | 0.0000000 |
| 498 | C4b | -12.261373 | -1.860676 | 0.0000000 | 0.0000000 |
| 19 | Hpca | 16.044706 | 1.853020 | 0.0000000 | 0.0000000 |
| 15 | Gria2 | 17.615229 | 1.823955 | 0.0000000 | 0.0000000 |
| 133 | Rspo1 | 3.309680 | 1.770562 | 0.0009340 | 0.0030130 |
| 26 | Vgf | 14.196186 | 1.742860 | 0.0000000 | 0.0000000 |
| 38 | Gria1 | 11.446211 | 1.620269 | 0.0000000 | 0.0000000 |
| 8 | Rbfox3 | 18.889765 | 1.608638 | 0.0000000 | 0.0000000 |
| 18 | Cx3cl1 | 16.199612 | 1.591508 | 0.0000000 | 0.0000000 |
| 13 | Syn1 | 18.047415 | 1.565465 | 0.0000000 | 0.0000000 |
| 489 | Enpp2 | -6.433960 | -1.483180 | 0.0000000 | 0.0000000 |
| 11 | Fam131a | 18.445550 | 1.470913 | 0.0000000 | 0.0000000 |
| 16 | Slc30a3 | 17.169088 | 1.469251 | 0.0000000 | 0.0000000 |
| 30 | Camk4 | 13.056713 | 1.399566 | 0.0000000 | 0.0000000 |
| 22 | Rph3a | 14.591459 | 1.344638 | 0.0000000 | 0.0000000 |
| 25 | Dkk3 | 14.273308 | 1.343871 | 0.0000000 | 0.0000000 |
| 60 | Zbtb20 | 8.227408 | 1.327582 | 0.0000000 | 0.0000000 |
| 84 | Nptx2 | 5.746940 | 1.290526 | 0.0000000 | 0.0000000 |
| 91 | Fosb | 5.356630 | 1.254899 | 0.0000001 | 0.0000004 |
| 78 | Plcxd2 | 6.373752 | 1.230456 | 0.0000000 | 0.0000000 |
| 131 | Krt73 | 3.381140 | 1.216898 | 0.0007219 | 0.0023590 |
| 155 | Pf4 | 2.591592 | 1.216042 | 0.0095533 | 0.0259601 |
| 132 | Cux2 | 3.340073 | 1.214608 | 0.0008376 | 0.0027194 |
| 80 | Lamp5 | 6.292746 | 1.208978 | 0.0000000 | 0.0000000 |
| 156 | Col11a1 | 2.537400 | 1.204545 | 0.0111679 | 0.0301836 |
| 41 | Tbr1 | 10.809135 | 1.203883 | 0.0000000 | 0.0000000 |
| 31 | Cpne6 | 12.727281 | 1.181772 | 0.0000000 | 0.0000000 |
| 24 | Smad3 | 14.521547 | 1.135137 | 0.0000000 | 0.0000000 |
| 23 | Brinp1 | 14.580751 | 1.133443 | 0.0000000 | 0.0000000 |
| 119 | Col6a1 | 4.020768 | 1.128259 | 0.0000580 | 0.0002117 |
| 87 | Lrrc55 | 5.482105 | 1.082896 | 0.0000000 | 0.0000002 |
| 102 | Igfbp6 | 4.866201 | 1.071764 | 0.0000011 | 0.0000049 |
| 71 | Chrm4 | 6.935808 | 1.067390 | 0.0000000 | 0.0000000 |
| 96 | Ccl6 | 5.152690 | 1.045405 | 0.0000003 | 0.0000012 |
| 151 | Pten | 2.766725 | 1.041025 | 0.0056622 | 0.0158163 |
| 17 | Pcdhgc5 | 16.407131 | 1.018808 | 0.0000000 | 0.0000000 |
| 54 | Rasgrf2 | 8.745890 | 1.013341 | 0.0000000 | 0.0000000 |
| 29 | Dclk3 | 13.192946 | 1.006109 | 0.0000000 | 0.0000000 |
6.1.4 PLX only, APP v.s. C6
Cell number compare: ‘APP’: 4264 ; ‘C6’: 7781
## [1] 4264
## [1] 7781
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 497 | App | -13.880145 | -9.670342 | 0.0000000 | 0.0000000 |
| 6 | Penk | 9.019672 | 4.652274 | 0.0000000 | 0.0000000 |
| 494 | Prkcd | -10.935171 | -4.382350 | 0.0000000 | 0.0000000 |
| 0 | Ppp1r1b | 13.985020 | 4.381724 | 0.0000000 | 0.0000000 |
| 7 | Adora2a | 8.980073 | 4.121275 | 0.0000000 | 0.0000000 |
| 454 | Calb2 | -5.245508 | -3.326567 | 0.0000002 | 0.0000011 |
| 473 | Plp1 | -7.015121 | -3.178985 | 0.0000000 | 0.0000000 |
| 480 | Synpo2 | -7.919139 | -3.133509 | 0.0000000 | 0.0000000 |
| 492 | Syp | -10.453685 | -2.940215 | 0.0000000 | 0.0000000 |
| 8 | Six3 | 8.773899 | 2.876801 | 0.0000000 | 0.0000000 |
| 493 | Tcf7l2 | -10.567602 | -2.757150 | 0.0000000 | 0.0000000 |
| 22 | Drd2 | 5.490453 | 2.562328 | 0.0000000 | 0.0000003 |
| 14 | Scn4b | 7.123028 | 2.416922 | 0.0000000 | 0.0000000 |
| 24 | Otof | 4.905724 | 2.416332 | 0.0000009 | 0.0000063 |
| 36 | Clic6 | 3.680038 | 2.291078 | 0.0002332 | 0.0011320 |
| 3 | Meis2 | 10.328524 | 2.274700 | 0.0000000 | 0.0000000 |
| 4 | Syndig1l | 10.225938 | 2.209832 | 0.0000000 | 0.0000000 |
| 425 | Gfap | -3.227096 | -2.203738 | 0.0012505 | 0.0053902 |
| 489 | Apoe | -9.520561 | -2.018902 | 0.0000000 | 0.0000000 |
| 487 | Slc17a7 | -9.024788 | -1.932678 | 0.0000000 | 0.0000000 |
| 495 | Plekhg1 | -12.166815 | -1.930067 | 0.0000000 | 0.0000000 |
| 499 | Mapt | -15.768661 | -1.908040 | 0.0000000 | 0.0000000 |
| 436 | Agt | -3.768015 | -1.868096 | 0.0001646 | 0.0008311 |
| 16 | Drd1 | 6.816484 | 1.840841 | 0.0000000 | 0.0000000 |
| 498 | Bin1 | -14.733479 | -1.773697 | 0.0000000 | 0.0000000 |
| 486 | Dkk3 | -9.008285 | -1.729258 | 0.0000000 | 0.0000000 |
| 464 | Cldn11 | -5.949452 | -1.651317 | 0.0000000 | 0.0000000 |
| 13 | Syt6 | 7.184234 | 1.627475 | 0.0000000 | 0.0000000 |
| 490 | Bsg | -9.645227 | -1.616300 | 0.0000000 | 0.0000000 |
| 470 | Lef1 | -6.515151 | -1.534849 | 0.0000000 | 0.0000000 |
| 496 | Cck | -12.275343 | -1.471486 | 0.0000000 | 0.0000000 |
| 403 | Klf4 | -2.506705 | -1.366731 | 0.0121862 | 0.0414498 |
| 450 | Sox10 | -4.795091 | -1.358600 | 0.0000016 | 0.0000108 |
| 462 | Vgf | -5.818213 | -1.304803 | 0.0000000 | 0.0000001 |
| 455 | Fibcd1 | -5.276342 | -1.271177 | 0.0000001 | 0.0000010 |
| 485 | Adgra1 | -8.345139 | -1.270859 | 0.0000000 | 0.0000000 |
| 444 | Dnm1 | -3.965817 | -1.247372 | 0.0000731 | 0.0004109 |
| 467 | Eno2 | -6.191310 | -1.209307 | 0.0000000 | 0.0000000 |
| 474 | Ptpru | -7.086030 | -1.188152 | 0.0000000 | 0.0000000 |
| 439 | Mfsd2a | -3.824056 | -1.120665 | 0.0001313 | 0.0006983 |
| 448 | Cbs | -4.523027 | -1.065574 | 0.0000061 | 0.0000396 |
| 38 | Col6a1 | 3.551789 | 1.063238 | 0.0003826 | 0.0017714 |
| 12 | Gng8 | 7.319304 | 1.035783 | 0.0000000 | 0.0000000 |
| 468 | Camk2a | -6.252263 | -1.015054 | 0.0000000 | 0.0000000 |
| 483 | Olig1 | -8.127840 | -1.014377 | 0.0000000 | 0.0000000 |
| 472 | Enpp2 | -6.950093 | -1.007070 | 0.0000000 | 0.0000000 |
| 431 | Gm2115 | -3.571424 | -1.003885 | 0.0003550 | 0.0016591 |
| 422 | Ntng1 | -3.125486 | -1.002546 | 0.0017751 | 0.0074585 |
6.2 APP only, PLX v.s. control
Here, we use Wilcoxon rank-sum to compute differential expression.
The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.
6.2.1 CA1-ProS
Cell number compare: ‘PLX’: 767 ; ‘Control’: 308
## [1] 767
## [1] 308
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 453 | App | -3.790594 | -8.404049 | 0.0001503 | 0.0015655 |
| 484 | Hpca | -5.712616 | -7.086289 | 0.0000000 | 0.0000003 |
| 472 | Grin1 | -4.930967 | -4.880014 | 0.0000008 | 0.0000146 |
| 499 | Wfs1 | -8.801627 | -4.490318 | 0.0000000 | 0.0000000 |
| 480 | Gria1 | -5.209080 | -4.333184 | 0.0000002 | 0.0000047 |
| 496 | Egr1 | -7.397917 | -4.266816 | 0.0000000 | 0.0000000 |
| 493 | Camk2a | -6.812467 | -3.609195 | 0.0000000 | 0.0000000 |
| 474 | Grin2a | -5.065786 | -3.468377 | 0.0000004 | 0.0000078 |
| 471 | Slc17a7 | -4.913042 | -3.412647 | 0.0000009 | 0.0000155 |
| 483 | Dnm1 | -5.587031 | -3.291272 | 0.0000000 | 0.0000007 |
| 485 | Syngap1 | -5.838311 | -2.977462 | 0.0000000 | 0.0000002 |
| 498 | Adgrl2 | -8.646818 | -2.619645 | 0.0000000 | 0.0000000 |
| 490 | Kcnab1 | -6.147386 | -2.514546 | 0.0000000 | 0.0000000 |
| 464 | Dkk3 | -4.318792 | -2.441522 | 0.0000157 | 0.0002179 |
| 497 | Gm2115 | -7.662667 | -2.386542 | 0.0000000 | 0.0000000 |
| 467 | Fam131a | -4.635037 | -2.316480 | 0.0000036 | 0.0000541 |
| 473 | Dlg4 | -5.046449 | -2.304920 | 0.0000005 | 0.0000083 |
| 444 | Ptk2b | -2.988303 | -2.287666 | 0.0028053 | 0.0246080 |
| 462 | Grin2b | -4.225038 | -2.073683 | 0.0000239 | 0.0003143 |
| 487 | Brinp1 | -6.024516 | -2.026201 | 0.0000000 | 0.0000001 |
| 486 | Cx3cl1 | -5.845807 | -1.972603 | 0.0000000 | 0.0000002 |
| 494 | Plxna1 | -6.875477 | -1.958254 | 0.0000000 | 0.0000000 |
| 469 | Fezf2 | -4.817223 | -1.814493 | 0.0000015 | 0.0000235 |
| 452 | Gria2 | -3.687388 | -1.800285 | 0.0002266 | 0.0023119 |
| 488 | Vgf | -6.063082 | -1.787795 | 0.0000000 | 0.0000001 |
| 451 | Cpne6 | -3.669137 | -1.729893 | 0.0002434 | 0.0024337 |
| 479 | Arc | -5.175402 | -1.725534 | 0.0000002 | 0.0000054 |
| 495 | Bcan | -6.943049 | -1.724560 | 0.0000000 | 0.0000000 |
| 489 | Epha10 | -6.107842 | -1.691080 | 0.0000000 | 0.0000000 |
| 476 | Nr4a1 | -5.087840 | -1.655490 | 0.0000004 | 0.0000073 |
| 465 | Nptx2 | -4.402769 | -1.585457 | 0.0000107 | 0.0001527 |
| 492 | Ptpru | -6.714150 | -1.518369 | 0.0000000 | 0.0000000 |
| 445 | Pthlh | -3.007206 | -1.448499 | 0.0026366 | 0.0235411 |
| 466 | Plekhg1 | -4.480988 | -1.426212 | 0.0000074 | 0.0001093 |
| 491 | Pkp2 | -6.250157 | -1.417509 | 0.0000000 | 0.0000000 |
| 450 | Eno2 | -3.643282 | -1.297289 | 0.0002692 | 0.0026391 |
| 481 | Sorl1 | -5.358457 | -1.292561 | 0.0000001 | 0.0000022 |
| 454 | Bin1 | -3.840568 | -1.265778 | 0.0001228 | 0.0013059 |
| 468 | Slc30a3 | -4.740199 | -1.238509 | 0.0000021 | 0.0000334 |
| 0 | Gfap | 4.052738 | 1.222129 | 0.0000506 | 0.0006173 |
| 446 | Nr4a2 | -3.032954 | -1.144256 | 0.0024217 | 0.0220157 |
| 478 | Robo1 | -5.153566 | -1.139854 | 0.0000003 | 0.0000058 |
| 482 | Cck | -5.390831 | -1.120382 | 0.0000001 | 0.0000019 |
| 440 | Sulf2 | -2.837188 | -1.081264 | 0.0045513 | 0.0373056 |
| 463 | Gria3 | -4.286744 | -1.071109 | 0.0000181 | 0.0002450 |
| 441 | Mink1 | -2.892919 | -1.029978 | 0.0038168 | 0.0318066 |
| 459 | Syn1 | -3.971585 | -1.005008 | 0.0000714 | 0.0008500 |
6.2.2 CA2
Cell number compare: ‘PLX’: 80 ; ‘Control’: 134.
## [1] 80
## [1] 134
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 499 | Zbtb20 | -4.593225 | -6.402827 | 0.0000044 | 0.0021822 |
| 498 | Gria1 | -3.936073 | -4.788919 | 0.0000828 | 0.0207065 |
| 496 | Syngap1 | -3.703331 | -3.032099 | 0.0002128 | 0.0265984 |
| 497 | Mapt | -3.742121 | -1.788793 | 0.0001825 | 0.0265984 |
6.2.3 CA3
Cell number compare: ‘PLX’: 397 ; ‘Control’: 425.
## [1] 397
## [1] 425
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 488 | Slc17a7 | -3.531298 | -3.199179 | 0.0004135 | 0.0159048 |
| 498 | Gria1 | -4.536818 | -3.075956 | 0.0000057 | 0.0009518 |
| 497 | Ptk2b | -4.382925 | -3.067826 | 0.0000117 | 0.0014637 |
| 490 | Zbtb20 | -3.716792 | -2.313827 | 0.0002018 | 0.0091713 |
| 495 | Syngap1 | -4.102038 | -1.647356 | 0.0000410 | 0.0034127 |
| 494 | Camk2a | -3.992094 | -1.639011 | 0.0000655 | 0.0045413 |
| 0 | Gfap | 4.927943 | 1.520422 | 0.0000008 | 0.0004155 |
| 486 | Dlg4 | -3.232332 | -1.368185 | 0.0012278 | 0.0409281 |
| 489 | Grm2 | -3.651531 | -1.106893 | 0.0002607 | 0.0108617 |
| 493 | Itga7 | -3.967401 | -1.072866 | 0.0000727 | 0.0045413 |
| 492 | Slc30a3 | -3.898465 | -1.043471 | 0.0000968 | 0.0053780 |
| 487 | Brinp1 | -3.368145 | -1.028354 | 0.0007568 | 0.0270270 |
6.2.4 DG
Cell number compare: ‘PLX’: 97 ; ‘Control’: 143
## [1] 97
## [1] 143
| names | scores | logfoldchanges | pvals | pvals_adj |
|---|---|---|---|---|
| NA | NA | NA | NA | NA |
| :—–: | :——: | :————–: | :—–: | :———: |
6.3 C6 only, PLX v.s. control
Here, we use Wilcoxon rank-sum to compute differential expression.
The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.
6.3.1 CA1-ProS
Cell number compare: ‘PLX’: 631 ; ‘Control’: 782
## [1] 631
## [1] 782
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 3 | App | 5.790393 | 12.891213 | 0.0000000 | 0.0000009 |
| 5 | Ptk2b | 5.396896 | 3.497551 | 0.0000001 | 0.0000048 |
| 0 | Camk2a | 7.807320 | 3.118698 | 0.0000000 | 0.0000000 |
| 2 | Zbtb20 | 6.761383 | 2.588190 | 0.0000000 | 0.0000000 |
| 17 | Nptx1 | 3.678650 | 2.354456 | 0.0002345 | 0.0058618 |
| 13 | Syp | 3.957265 | 2.335203 | 0.0000758 | 0.0023691 |
| 22 | Grin1 | 3.002997 | 2.255974 | 0.0026734 | 0.0495065 |
| 4 | Cpne6 | 5.597284 | 2.194341 | 0.0000000 | 0.0000018 |
| 15 | Fibcd1 | 3.877071 | 1.937821 | 0.0001057 | 0.0029367 |
| 10 | Nr4a2 | 4.180668 | 1.776978 | 0.0000291 | 0.0011179 |
| 1 | Nefm | 7.410151 | 1.633473 | 0.0000000 | 0.0000000 |
| 6 | Bin1 | 4.788848 | 1.231143 | 0.0000017 | 0.0000932 |
| 498 | Adgrl2 | -5.072906 | -1.074066 | 0.0000004 | 0.0000245 |
| 14 | Nptxr | 3.909660 | 1.073459 | 0.0000924 | 0.0027184 |
| 499 | Bcan | -5.636889 | -1.030305 | 0.0000000 | 0.0000017 |
6.3.2 CA2
Cell number compare: ‘PLX’: 117 ; ‘Control’: 118.
## [1] 117
## [1] 118
| names | scores | logfoldchanges | pvals | pvals_adj |
|---|---|---|---|---|
| NA | NA | NA | NA | NA |
| :—–: | :——: | :————–: | :—–: | :———: |
6.3.3 CA3
Cell number compare: ‘PLX’: 896 ; ‘Control’: 486 .
## [1] 896
## [1] 486
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 6 | App | 5.988654 | 12.676558 | 0.0000000 | 0.0000001 |
| 2 | Col6a1 | 7.440753 | 7.732464 | 0.0000000 | 0.0000000 |
| 3 | Plagl1 | 7.309687 | 5.100309 | 0.0000000 | 0.0000000 |
| 12 | Syp | 4.902721 | 4.119861 | 0.0000009 | 0.0000315 |
| 5 | Nptxr | 6.027261 | 3.850422 | 0.0000000 | 0.0000001 |
| 23 | Nptx1 | 3.806060 | 3.482384 | 0.0001412 | 0.0024345 |
| 16 | Cpne6 | 4.522863 | 3.188512 | 0.0000061 | 0.0001525 |
| 1 | Nr2f2 | 7.861829 | 3.170705 | 0.0000000 | 0.0000000 |
| 9 | Zbtb20 | 5.425078 | 2.983680 | 0.0000001 | 0.0000024 |
| 4 | Nnat | 7.298112 | 2.638367 | 0.0000000 | 0.0000000 |
| 0 | Crtac1 | 8.777737 | 2.481828 | 0.0000000 | 0.0000000 |
| 15 | Tcerg1l | 4.682373 | 2.331260 | 0.0000028 | 0.0000746 |
| 11 | Fosl2 | 4.998215 | 2.150707 | 0.0000006 | 0.0000207 |
| 37 | Col5a2 | 2.900386 | 1.911841 | 0.0037270 | 0.0404421 |
| 8 | Adgra1 | 5.431007 | 1.688240 | 0.0000001 | 0.0000024 |
| 497 | Brinp1 | -4.684701 | -1.567339 | 0.0000028 | 0.0000746 |
| 10 | Fezf2 | 5.063077 | 1.438733 | 0.0000004 | 0.0000159 |
| 27 | Eno2 | 3.582112 | 1.423155 | 0.0003408 | 0.0050122 |
| 26 | Ptpru | 3.591781 | 1.403387 | 0.0003284 | 0.0049761 |
| 20 | Bin1 | 4.233982 | 1.357217 | 0.0000230 | 0.0004783 |
| 31 | Rspo2 | 3.264999 | 1.326645 | 0.0010946 | 0.0144032 |
| 18 | Syt17 | 4.318748 | 1.322203 | 0.0000157 | 0.0003507 |
| 13 | Cnr1 | 4.840188 | 1.249465 | 0.0000013 | 0.0000405 |
| 22 | Dlg4 | 3.877839 | 1.233872 | 0.0001054 | 0.0018819 |
| 34 | Dkk3 | 3.054461 | 1.182020 | 0.0022547 | 0.0262169 |
| 7 | Kit | 5.462627 | 1.169676 | 0.0000000 | 0.0000023 |
| 17 | Mink1 | 4.349097 | 1.119043 | 0.0000137 | 0.0003255 |
| 495 | Bcan | -3.988084 | -1.110037 | 0.0000666 | 0.0012335 |
| 492 | Fam131a | -3.064624 | -1.071578 | 0.0021794 | 0.0259457 |
| 24 | Cplx1 | 3.787991 | 1.063867 | 0.0001519 | 0.0025312 |
| 498 | Epha7 | -6.492026 | -1.017116 | 0.0000000 | 0.0000000 |
6.3.4 DG
Cell number compare: ‘PLX’: 145 ; ‘Control’: 102
## [1] 145
## [1] 102
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 499 | Hpca | -4.845665 | -4.467802 | 1.30e-06 | 0.0006309 |
| 498 | Nefm | -4.325647 | -2.383967 | 1.52e-05 | 0.0038021 |
6.4 PLX only, APP v.s. C6
Here, we use Wilcoxon rank-sum to compute differential expression.
The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.
6.4.1 CA1-ProS
Cell number compare: ‘APP’: 782 ; ‘C6’: 308
## [1] 782
## [1] 308
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 486 | App | -3.770907 | -9.130591 | 0.0001627 | 0.0058091 |
| 487 | Dkk3 | -3.893462 | -3.569085 | 0.0000988 | 0.0038009 |
| 490 | Ptk2b | -3.991229 | -3.138422 | 0.0000657 | 0.0030493 |
| 498 | Kcnab1 | -5.636379 | -2.779752 | 0.0000000 | 0.0000043 |
| 491 | Egr1 | -4.484122 | -2.677108 | 0.0000073 | 0.0004067 |
| 497 | Camk2a | -5.035248 | -2.604655 | 0.0000005 | 0.0000740 |
| 475 | Slc17a7 | -3.094340 | -2.199769 | 0.0019725 | 0.0394502 |
| 488 | Syngap1 | -3.965692 | -1.918197 | 0.0000732 | 0.0030493 |
| 495 | Wfs1 | -4.780948 | -1.859754 | 0.0000017 | 0.0001745 |
| 477 | Cpne6 | -3.162617 | -1.731729 | 0.0015636 | 0.0339909 |
| 499 | Ptpru | -5.858304 | -1.600056 | 0.0000000 | 0.0000023 |
| 494 | Gm2115 | -4.734789 | -1.563882 | 0.0000022 | 0.0001827 |
| 480 | Fezf2 | -3.289980 | -1.553409 | 0.0010019 | 0.0250486 |
| 489 | Fibcd1 | -3.970393 | -1.508155 | 0.0000718 | 0.0030493 |
| 483 | Nr4a2 | -3.604116 | -1.466884 | 0.0003132 | 0.0092123 |
| 482 | Eno2 | -3.514683 | -1.357158 | 0.0004403 | 0.0122300 |
| 481 | Bin1 | -3.483804 | -1.201917 | 0.0004943 | 0.0130090 |
| 493 | Cck | -4.631894 | -1.159318 | 0.0000036 | 0.0002588 |
| 492 | Pkp2 | -4.495555 | -1.100752 | 0.0000069 | 0.0004067 |
| 476 | Arc | -3.120198 | -1.069206 | 0.0018073 | 0.0376520 |
| 484 | Cx3cl1 | -3.613625 | -1.068221 | 0.0003019 | 0.0092123 |
6.4.2 CA2
Cell number compare: ‘APP’: 80 ; ‘C6’: 117.
## [1] 80
## [1] 117
| names | scores | logfoldchanges | pvals | pvals_adj |
|---|---|---|---|---|
| NA | NA | NA | NA | NA |
| :—–: | :——: | :————–: | :—–: | :———: |
6.4.3 CA3
Cell number compare: ‘APP’: 397 ; ‘C6’: 896.
## [1] 397
## [1] 896
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 497 | App | -7.835498 | -15.362594 | 0.0000000 | 0.0000000 |
| 496 | Col6a1 | -7.786898 | -9.011167 | 0.0000000 | 0.0000000 |
| 495 | Syp | -7.782215 | -6.274181 | 0.0000000 | 0.0000000 |
| 494 | Plagl1 | -7.692765 | -5.432734 | 0.0000000 | 0.0000000 |
| 481 | Slc17a7 | -5.761420 | -5.392075 | 0.0000000 | 0.0000002 |
| 489 | Gria1 | -6.725518 | -4.194874 | 0.0000000 | 0.0000000 |
| 479 | Cpne6 | -5.430500 | -3.738366 | 0.0000001 | 0.0000013 |
| 484 | Nptxr | -5.961231 | -3.659163 | 0.0000000 | 0.0000001 |
| 492 | Nr2f2 | -6.948338 | -3.652885 | 0.0000000 | 0.0000000 |
| 477 | Ptk2b | -5.365188 | -3.382440 | 0.0000001 | 0.0000018 |
| 488 | Zbtb20 | -6.275761 | -3.091775 | 0.0000000 | 0.0000000 |
| 471 | Tcerg1l | -5.019657 | -3.009680 | 0.0000005 | 0.0000089 |
| 498 | Eno2 | -7.994298 | -2.813303 | 0.0000000 | 0.0000000 |
| 451 | Hpca | -3.295550 | -2.758693 | 0.0009823 | 0.0091032 |
| 499 | Crtac1 | -8.839882 | -2.670600 | 0.0000000 | 0.0000000 |
| 443 | Col5a2 | -3.046008 | -2.446339 | 0.0023190 | 0.0190083 |
| 490 | Bin1 | -6.795108 | -2.402109 | 0.0000000 | 0.0000000 |
| 463 | Ptpru | -4.331661 | -2.399196 | 0.0000148 | 0.0001897 |
| 486 | Nnat | -6.038895 | -2.376615 | 0.0000000 | 0.0000001 |
| 456 | Calb2 | -3.747809 | -2.271042 | 0.0001784 | 0.0018977 |
| 493 | Sulf2 | -7.190452 | -2.213496 | 0.0000000 | 0.0000000 |
| 480 | Syngap1 | -5.443014 | -2.063145 | 0.0000001 | 0.0000013 |
| 473 | Fosl2 | -5.076895 | -1.972176 | 0.0000004 | 0.0000071 |
| 487 | Adgra1 | -6.107032 | -1.923982 | 0.0000000 | 0.0000000 |
| 462 | Camk2a | -4.322134 | -1.801131 | 0.0000155 | 0.0001932 |
| 482 | Plxna1 | -5.791290 | -1.762644 | 0.0000000 | 0.0000002 |
| 474 | Vgf | -5.162310 | -1.751491 | 0.0000002 | 0.0000047 |
| 461 | Dkk3 | -4.254239 | -1.733265 | 0.0000210 | 0.0002558 |
| 470 | Dlg4 | -4.958462 | -1.678501 | 0.0000007 | 0.0000118 |
| 467 | Fam107a | -4.798694 | -1.630923 | 0.0000016 | 0.0000242 |
| 466 | Fezf2 | -4.604373 | -1.484388 | 0.0000041 | 0.0000608 |
| 459 | Gria2 | -4.013981 | -1.484091 | 0.0000597 | 0.0006942 |
| 476 | Cnr1 | -5.238116 | -1.446475 | 0.0000002 | 0.0000034 |
| 468 | Cplx1 | -4.833812 | -1.420296 | 0.0000013 | 0.0000209 |
| 478 | Mas1 | -5.408137 | -1.404513 | 0.0000001 | 0.0000014 |
| 491 | Bsg | -6.816099 | -1.372706 | 0.0000000 | 0.0000000 |
| 485 | Neto1 | -5.993039 | -1.369099 | 0.0000000 | 0.0000001 |
| 483 | Cck | -5.833997 | -1.290572 | 0.0000000 | 0.0000002 |
| 469 | Mapt | -4.885723 | -1.212052 | 0.0000010 | 0.0000166 |
| 472 | Syn1 | -5.041131 | -1.208403 | 0.0000005 | 0.0000083 |
| 0 | Dclk3 | 4.588468 | 1.134732 | 0.0000045 | 0.0000638 |
| 458 | Mink1 | -3.891834 | -1.115539 | 0.0000995 | 0.0011054 |
| 440 | Hcn1 | -2.906746 | -1.103341 | 0.0036521 | 0.0280931 |
| 475 | Camk4 | -5.188063 | -1.063567 | 0.0000002 | 0.0000042 |
| 449 | Nefm | -3.262853 | -1.062377 | 0.0011030 | 0.0100270 |
6.4.4 DG
Cell number compare: ‘APP’: 97 ; ‘C6’: 145
## [1] 97
## [1] 145
| names | scores | logfoldchanges | pvals | pvals_adj |
|---|---|---|---|---|
| NA | NA | NA | NA | NA |
| :—–: | :——: | :————–: | :—–: | :———: |
6.5 Control only, APP v.s. C6
Here, we use Wilcoxon rank-sum to compute differential expression.
The statistical significance was cut-off by log2(FoldChange) > 1 and p_adj < 0.05.
6.5.1 CA1-ProS
Cell number compare: ‘APP’: 631 ; ‘C6’: 767
## [1] 631
## [1] 767
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 8 | App | 5.781549 | 12.164670 | 0.0000000 | 0.0000004 |
| 6 | Grin1 | 6.183330 | 5.227798 | 0.0000000 | 0.0000000 |
| 0 | Camk2a | 10.005967 | 4.123237 | 0.0000000 | 0.0000000 |
| 3 | Grin2a | 7.332690 | 4.090010 | 0.0000000 | 0.0000000 |
| 15 | Egr1 | 5.379902 | 3.774128 | 0.0000001 | 0.0000023 |
| 38 | Gria1 | 3.939990 | 3.099695 | 0.0000815 | 0.0010447 |
| 1 | Zbtb20 | 7.940286 | 3.059491 | 0.0000000 | 0.0000000 |
| 2 | Grin2b | 7.342675 | 2.918111 | 0.0000000 | 0.0000000 |
| 12 | Dnm1 | 5.535995 | 2.691057 | 0.0000000 | 0.0000012 |
| 35 | Ptk2b | 4.026789 | 2.646795 | 0.0000565 | 0.0007853 |
| 7 | Nr4a1 | 5.904626 | 2.390820 | 0.0000000 | 0.0000002 |
| 11 | Gria2 | 5.614274 | 2.240807 | 0.0000000 | 0.0000008 |
| 5 | Cpne6 | 6.198639 | 2.192505 | 0.0000000 | 0.0000000 |
| 43 | Syp | 3.662617 | 2.026821 | 0.0002497 | 0.0028369 |
| 13 | Dlg4 | 5.447664 | 1.948673 | 0.0000001 | 0.0000018 |
| 24 | Syngap1 | 4.567688 | 1.936160 | 0.0000049 | 0.0000986 |
| 32 | Arc | 4.125836 | 1.809557 | 0.0000369 | 0.0005597 |
| 57 | Wfs1 | 3.183090 | 1.780875 | 0.0014571 | 0.0125614 |
| 10 | Brinp1 | 5.710459 | 1.653508 | 0.0000000 | 0.0000005 |
| 4 | Nptxr | 6.339089 | 1.559325 | 0.0000000 | 0.0000000 |
| 26 | Vgf | 4.515103 | 1.455290 | 0.0000063 | 0.0001172 |
| 48 | Nr4a2 | 3.444421 | 1.454350 | 0.0005723 | 0.0058396 |
| 47 | Fam131a | 3.448548 | 1.407428 | 0.0005636 | 0.0058396 |
| 21 | Gm2115 | 4.696423 | 1.405113 | 0.0000026 | 0.0000602 |
| 17 | Bin1 | 5.228735 | 1.295003 | 0.0000002 | 0.0000047 |
| 25 | Mink1 | 4.520494 | 1.203446 | 0.0000062 | 0.0001172 |
| 41 | Cx3cl1 | 3.697697 | 1.134877 | 0.0002176 | 0.0025901 |
| 22 | Itga7 | 4.639245 | 1.128132 | 0.0000035 | 0.0000759 |
| 30 | Rbfox3 | 4.291780 | 1.117081 | 0.0000177 | 0.0002859 |
| 27 | Epha10 | 4.463782 | 1.086565 | 0.0000081 | 0.0001411 |
| 9 | Robo1 | 5.722574 | 1.075899 | 0.0000000 | 0.0000005 |
| 16 | Crhr1 | 5.349482 | 1.002607 | 0.0000001 | 0.0000026 |
6.5.2 CA2
Cell number compare: ‘APP’: 134 ; ‘C6’: 118.
## [1] 134
## [1] 118
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 0 | Zbtb20 | 3.913356 | 4.014938 | 9.1e-05 | 0.0455112 |
6.5.3 CA3
Cell number compare: ‘APP’: 425 ; ‘C6’: 486
## [1] 425
## [1] 486
| names | scores | logfoldchanges | pvals | pvals_adj | |
|---|---|---|---|---|---|
| 1 | Nptx1 | 3.908714 | 2.874441 | 9.28e-05 | 0.0115986 |
| 498 | Sulf2 | -4.217771 | -1.168880 | 2.47e-05 | 0.0041121 |
| 0 | Smad3 | 4.683566 | 1.105830 | 2.80e-06 | 0.0014096 |
6.5.4 DG
Cell number compare: ‘APP’: 143 ; ‘C6’: 102
## [1] 143
## [1] 102
| names | scores | logfoldchanges | pvals | pvals_adj |
|---|---|---|---|---|
| NA | NA | NA | NA | NA |
| :—–: | :——: | :————–: | :—–: | :———: |
–>
–>
–>
–>
Abbreviation
Cell types & Regions
Astro, Astrocyte;
ABC, arachnoid barrier cells;
BAM, border-associated macrophages;
BLA, Basolateral amygdala;
CB, cerebellum;
CGE, caudal ganglionic eminence;
CHOR, choroid plexus;
CNU, cerebral nuclei;
CR, Cajal–Retzius;
CT, corticothalamic;
CTX, cerebral cortex;
CTXsp, cortical subplate;
DC, dendritic cells;
DCO, dorsal cochlear nucleus;
DG, dentate gyrus;
EA, extended amygdala;
Endo, endothelial cells;
ENT, Entorhinal area;
ENTl, Entorhinal area, lateral part;
Epen, ependymal;
EPI, epithalamus;
ET, extratelencephalic;
GC, granule cell;
HB, hindbrain;
HPF, hippocampal formation;
HY, hypothalamus;
HYa, anterior hypothalamic;
IMN, immature neurons;
IT, intratelencephalic;
L6b, layer 6b;
LGE, lateral ganglionic eminence;
LH, lateral habenula;
LSX, lateral septal complex;
MB, midbrain;
MGE, medial ganglionic eminence;
MH, medial habenula;
MM, medial mammillary nucleus;
MY, medulla;
NN, non-neuronal;
NP, near-projecting;
NT, non-telencephalon;
OB, olfactory bulb;
OEC, olfactory ensheathing cells;
OLF, olfactory areas;
Oligo, oligodendrocytes;
OPC, oligodendrocyte precursor cells;
P, pons;
PAL, pallidum;
Peri, pericytes;
PIR, piriform cortex;
SMC, smooth muscle cells;
STR, striatum;
TE, telencephalon;
TH, thalamus;
UBC, unipolar brush cells;
VLMC, vascular leptomeningeal cells.
Neurotransmitter types
Chol, cholinergic;
Dopa, dopaminergic;
GABA, GABAergic;
Glut, glutamatergic;
Glyc, glycinergic;
Hist, histaminergic;
Nora, noradrenergic;
Sero, serotonergic